So, which of the two would be the best choice to install Windows Server 2008 Standard and how well would it perform on the above mentioned specs (CPU, RAM, GPU & HD)?
It will be the main Server for Active Directory / Domain Controller, DNS, DHCP, and File Sharing, in a Network Domain of 20 PCs.

P.S.
What's this (All Solid Capacitor Design) reference for the GA-P35-DS3L/S3L Intel P35 + ICH9 Chipset M/B?
Does it mean that it has better capacitors and that it will last much longer?
If that’s the case, it might be the better choice, as this server will be continuously working all day and night non stop.

Re: Which of these 2 Motherboards/Rigs,for Windows Server 2008 Standard?

All solid capacitors will not leak like electrolyte capacitors and can withstand higher temperatures too. Also IIRC the P35 should have better I/O performance than the P31 so I would go for your first setup.